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You can avoid the heartbreak of bad canonicalization, or at least minimize it, by doing a few simple things:

1. Use 301 redirection to ensure that your home page is only found at one URL. If you don’t know how, read Stephan Spencer’s column about rewrites and redirects.
2. Link consistently to your home page from within your own site. Use a single URL for your home page. Don’t mix in instances of ‘www.iansnerdvana.com/index.html’ with ‘www.iansnerdvana.com’. If you aren’t doing this properly right now, a quick change may have a big impact on SEO.
3. Don’t use tracking IDs in internal site navigation. A lot of sites add stuff like ‘?source=blog’ in their navigation. That lets them use their analytics reports to track user movement within, to and from their site. Instead, learn to use your web analytics referrer and navigation path reports. If you must use tracking IDs, change your software to use a hash mark (a ‘#’ sign) instead of a question mark. Search engines ignore everything after the hash, so you’ll avoid confusion.
4. Don’t use tracking IDs in organic links from other sites. If you get a link on another site, and want it to help with your SEO, don’t put a tracking ID in that, either.
5. Be careful with pagination. Many sites have pagination, where visitors can click a 1, 2, 3 etc. to jump to later pages in search results, product lists or articles. That’s fine, but make sure that the each page has a single URL. For example, if page 1 of the article is ‘www.iansnerdvana.com/article.html’ when I click the article link from the home page, make sure that the number ‘1′ in the pagination takes me there, too, instead of to ‘www.iansnerdvana.com/article.html?page=1′.
6. Set up preventative redirects. Make sure that ‘iansnerdvana.com’ 301 redirects to ‘www.iansnerdvana.com’.
7. Exclude ‘e-mail a friend’ pages. Most content management systems that have ‘e-mail a friend’ options direct the user to a unique page that has the same form and content. But every instance of that page has a unique URL like ‘ID=123′, to tell the server which product or article to forward. It’s canonical higgeldy-piggeldy. Use robots.txt and the meta robots tag to exclude these from search engine crawls.
8. Use common sense when building your site. Think, man/woman! If you need to change the header, footer or other page element based on where on your site the visitor came from, do it with cookies, or by sniffing out the referring URL. Design to do this ahead of time.